Monitoring genetic change in natural populations

1. Monitoring genetic change in natural populations Michael S. SchwartzU.S. Forest Service Fred W. AllendorfUniversity of Montana

2. First Working Group jointly funded by NCEAS & NESCent. Initial meeting in March 2008.

3. Objectives of Working Group (1) Provide practical guidelines for resource managers and policy makers to design genetic programs to monitor population trends and processes. (2) Evaluate potential to use genetic monitoring of candidate genes likely to be affected by climate change, and other types of stress, to understand evolutionary responses to environmental changes.

5. Trends in Ecology & Evolution 22:25-33. 2007. We define genetic monitoring as quantifying temporal changes in population genetic metrics or other population data. We distinguish monitoring, which must have a temporal dimension, from assessment, which reflects a snapshot of population characteristics at a single point in time.

6. Population Genetics in Space & Time Space: Describing patterns of genetic variation among geographical populations. FST,heterozygosity, allelic diversity Time: Describing changes in patterns of genetic variation among samples collected at different times from a single site. Fk, etc.

7. Schwartz et al. 2007

8. Schwartz et al. 2007

9. Class III: Detect and monitor adaptation (e.g., response to climate change) using candidate genes Using genetic markers to predict and monitor climate change in insects Carla Sgro & Ary Hoffmann

10. Three Examples • Class I: Detecting recolonization of lynx in Minnesota. • Class II: Estimation of effective population size in Swedish brown trout. • (3) Use of historical DNA to monitor genetic variation and manage grizzly bears in the Yellowstone Ecosystem (YE).

12. Genetics of Lynx in Minnesota Schwartz et al. 2004

13. Lynx Listed as Threatened • in March 2000 • Species occurs on 110 • Million acres of USFS land • Elusive, Patchily Distrib., • cyclic in abundance • In MN they were absent • from 1993-2001

14. Last verified 1993 McKelvey et al. 2000

15. How do we confirm lynx’s return to Minnesota after 10 yr absence? and Can we monitor the population using DNA?

16. Our Approach • Between 2002 - 2006 backtracked • “putative lynx” Schwartz et al. 2004 McKelvey et al. 2006

17. Track Surveys 2002 - 2006 back-tracked “putative” lynx

18. Backtracking Collected 263 scats and hairs (and tissue) Goal was to identify to species, then individual Schwartz et al. 2004

19. Lynx in Minnesota 263 samples 94.1% success scat / 70.0% success hair 157 confirmed lynx Schwartz et al. Unpub.

20. Lynx in Minnesota But is it 157 Individuals or Less? Schwartz et al. Unpub.

21. Focus on ~100-200bp PCR DNA + Sample 1 Sample 2 Sample 3 Sample 4 Sample 5 Sample 6 Sample 7 Sample 8 6-Microsatellite DNA Panel

22. 94 Unique lynx

24. Genetic Tools Also Provide Gender Identification Pilgrim et al. 2005

25. These Data Can be Turned Into a Corrected Index

26. All Metrics Suggest that Lynx are Increasing, But Indices may be Effort Sensitive

28. Lynx Effective Pop. Size (Same Raw Data) • Effort less imp. Methods: Tallmon et al. 2005, Tallmon et al. In Prep.

29. All Metrics Point to Same Trend

31. Conservation Genetics 4:249-264. 2003.

32. EFFECTIVE POPULATION SIZE (Ne) is the size of the ideal population (N) that will result in the same amount of genetic drift as in the actual population being considered. per generation:∆ h = -1/2N = F Ne can be estimated by using changes in allele frequencies over time to estimate F.

33. Sampled 100 fish from two sites annually from 1980-2000. Identified cohorts using otoliths to determine age. Examined 17 polymorphic allozyme loci

34. Geography: FST = 0.13 (stable over time) Temporal changes: Fk = based upon mean allele frequency change between consecutive cohorts (overlapping generations)

35. Site II Ne=48 I Ne=19 Point estimates of Ne for pairs of consecutive cohorts are relatively stable over time.

37. (3) Use of genetic monitoring to manage grizzly bears NCDE YE

38. Why do Yellowstone Ecosystem bears (YE) have 21% less nuclear heterozygosity and 61% less mtDNA diversity compared to the nearby Northern Continental Divide Ecosystem (NCDE) bears?

39. Continuous habitat ~150 km

40. Time Travel: The polymerase chain reaction (PCR) allows using historical or ancient DNA to detect genetic changes (or lack thereof) by going back in time using museum specimens or other sources of DNA (seed banks, fish scales, etc.). Miller & Waits (2003) used bone from museum specimens of grizzly bear skulls to extract DNA.

41. Proc. Natl. Acad. Sci. USA 100:4334-4339. 2003. A, B, or C???

42. And the answer is - Het: 0.564 0.560 0.544 Ne ~ 75 Ne ~ 50

43. Ongoing Genetic Monitoring Continued genetic screening of YE grizzly bears with microsatellite loci to detect migrant individuals using “assignment” tests to identify population of origin based upon genotype (YE or NCDE; FST =0.12) If no genetic exchange is detected by 2020, two bears will be translocated every generation (10 years) from the NCDE to the YE.

44. 1 Feb Introduction – Schwartz & Allendorf8 Feb 15 Feb Monitoring of Ne - Gordon Luikart22 Feb Snake River cutthroat trout - Mark Novak29 Feb Happy Birthday Janean!7 Mar 14 Mar 21 Mar ----4 Apr 11 Apr 18 Apr 25 Apr 2 May